Background Observational studies have consistently reported severe weight gains during the college years; information about the effect on body composition is scarce, however. Thus, the aim of the study was to determine the effect of exercise changes on body composition during 5 years at university. Methods Sixty-one randomly selected male and female dental (DES; 21 ± 3 years., 22 ± 2 kg/m2) and 53 sport (physical education) students (SPS; 20 ± 2 years., 22 ± 3 kg/m2) were accompanied over their 5-year study program. Body mass and body composition as determined via Dual-Energy x-ray-absorptiometry (DXA) at baseline and follow-up were selected as primary study endpoints. Confounding parameters (i.e., nutritional intake, diseases, medication) that may affect study endpoints were determined every two years. Endpoints were log-transformed to stabilize variance and achieve normal distributed values. Paired t-tests and unpaired Welch-t-tests were used to check intra and inter-group differences. Results Exercise volume decreased significantly by 33 % (p < .001) in the DES and increased significantly (p < .001) in the SPS group. Both cohorts comparably (p = .214) gained body mass (SPS: 1.9 %, 95 %-CI: 0.3−3.5 %, p = .019 vs. DES: 3.4 %, 1.4−5.5 %, p = .001). However, the increase in the SPS group can be completely attributed to changes in LBM (2.3 %, 1.1−3.5 %, p < 0.001) with no changes of total fat mass (0.6 %, −5.0−6.5 %, p = 0.823), while DES gained total FM and LBM in a proportion of 2:1. Corresponding changes were determined for appendicular skeletal muscle mass and abdominal body-fat. Maximum aerobic capacity increased (p = .076) in the SPS (1.6 %, −0.2−3.3 %) and significantly decreased (p = .004) in the DES (−3.3 %, −5.4 to −1.2 %). Group differences were significant (p < .001). With respect to nutritional intake or physical activity, no relevant changes or group differences were observed. Conclusion We conclude that the most deleterious effect on fatness and fitness in young college students was the pronounced decreases in exercise volume and particularly exercise intensity. Trial registration NCT00521235; “Effect of Different Working Conditions on Risk Factors in Dentists Versus Trainers. A Combined Cross sectional and Longitudinal Trial with Student and Senior Employees.”; August 24, 2007.